Yuqing TCR-seq preprocessing
Sung Rye Park
2023-09-27
Import data
Doublets were removed and clonotypes were selected by “1 alpha and 1 beta chain”.
Fig H
Clonotypes were filtered by “1 alpha and 1 beta chain”
M6 Clonotype Distribution
Table
Clonotypes : ones with 1 alpha and 1 beta chain
## Sample Frequency_of_clonotype number
## 1 M6 freq >= 5 0
## 2 M6 2 <= freq < 5 8
## 3 M6 freq = 1 1111
## 4 M6 total 1119M7 Clonotype Distribution
Table
Clonotypes : ones with 1 alpha and 1 beta chain
## Sample Frequency_of_clonotype number
## 1 M7 freq >= 5 0
## 2 M7 2 <= freq < 5 22
## 3 M7 freq = 1 1186
## 4 M7 total 1208Clustering
Cluster based on the resolutions
resolution_values <- c(0.2, 0.4, 0.8, 1)Clusters with the different resolutions
Find markers
Markers based on clustering-resolutions : 0.2, 0.4, 0.8, 1
Marker genes
resolution 0.2
Download cluster marker file
## [1] "RNA_snn_res.0.2"resolution 0.4
Download cluster marker file
## [1] "RNA_snn_res.0.4"resolution 0.8
Download cluster marker file
## [1] "RNA_snn_res.0.8"resolution 1
Download cluster marker file
## [1] "RNA_snn_res.1"
Cluster annotation
You can annotate each cluster using the table provided below.
## [1] "RNA_snn_res.0.2"
You can annotate each cluster using the table provided below.
## [1] "RNA_snn_res.0.4"
You can annotate each cluster using the table provided below.
## [1] "RNA_snn_res.0.8"
You can annotate each cluster using the table provided below.
## [1] "RNA_snn_res.1"
Recolor UMAP with resolution 0.2 clustering and annotation
## cluster Annotation color
## 1 cluster0 MDSC #28B463
## 2 cluster1 Neutrophil #3482DB
## 3 cluster2 Monocyte related #5CD3F6
## 4 cluster3 T cell #FA8072
## 5 cluster4 Red blood cell #F65CCC
## 6 cluster5 B cell #9C640C
## 7 cluster6 Red blood cell #F65CCC
## 8 cluster7 NK cell #8E44AD
## 9 cluster8 Macrophage/Dendritic cell #FF9033
## 10 cluster9 Basophil #1A5276
## 11 cluster10 #FDFEFE